removed debug message

[biopieces.git] / bp_bin / read_blast_tab

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
index c8c800fbc01100b8cd9e82c26358933e470ca42e..26d40890f02ee2327158e338dec67c7a1c486dee 100755 (executable)
--- a/bp_bin/read_blast_tab
+++ b/bp_bin/read_blast_tab
@@ -1,6 +1,125 @@
 #!/usr/bin/env perl
 
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read BLAST records in tabular format from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $file, $record, $line, @fields, $data_in, $num );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0'   },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+    $num = 1;
+
+    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+    while ( $line = <$data_in> )
+    {
+        chomp $line;
+
+        next if $line =~ /^#/;
+
+        @fields = split /\t/, $line;
+
+        $record->{ "REC_TYPE" }   = "BLAST";
+        $record->{ "Q_ID" }       = $fields[ 0 ];
+        $record->{ "S_ID" }       = $fields[ 1 ];
+        $record->{ "IDENT" }      = $fields[ 2 ];
+        $record->{ "ALIGN_LEN" }  = $fields[ 3 ];
+        $record->{ "MISMATCHES" } = $fields[ 4 ];
+        $record->{ "GAPS" }       = $fields[ 5 ];
+        $record->{ "Q_BEG" }      = $fields[ 6 ] - 1; # BLAST is 1-based
+        $record->{ "Q_END" }      = $fields[ 7 ] - 1; # BLAST is 1-based
+        $record->{ "S_BEG" }      = $fields[ 8 ] - 1; # BLAST is 1-based
+        $record->{ "S_END" }      = $fields[ 9 ] - 1; # BLAST is 1-based
+        $record->{ "E_VAL" }      = $fields[ 10 ];
+        $record->{ "BIT_SCORE" }  = $fields[ 11 ];
+
+        if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
+        {
+            $record->{ "STRAND" } = '-';
+
+            ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
+        }
+        else
+        {
+            $record->{ "STRAND" } = '+';
+        }
+
+        Maasha::Biopieces::put_record( $record, $out );
+
+        last if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
+    }
+
+    close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::Biotools;
+__END__